Method of separating microorganism using nonplanar solid substrate and device for separating microorganism using the same

ABSTRACT

Provided is a method of separating microorganisms from a sample including contacting the sample containing microorganisms with an inorganic ion exchange material such that the sample reacts with the inorganic ion exchange material, and contacting the reacted sample with a means for capturing microorganisms.

This application claims the benefit of Korean Patent Application Nos.10-2006-0079053, 10-2006-0079054, 10-2006-0079055, and 10-2006-0079056,each filed on 21 Aug. 2006, and 10-2006-0092919, filed on Sep. 25, 2006,in the Korean Intellectual Property Office, the disclosure of each ofwhich is incorporated herein in its entirety by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a method of separating microorganismsfrom a sample using ion exchange and a means for capturingmicroorganisms, a container for pretreating a sample containingmicroorganisms, and a device for separating microorganisms.

2. Description of the Related Art

Methods of separating microorganisms from a sample includecentrifugation and filtration. Further, in a method of concentrating andseparating particular cells, the cells are allowed to bind specificallyto receptors or ligands attached to a surface of a support. For example,an affinity chromatography method includes flowing a sample containingcells over a support to which antibodies capable of specifically bindingto the cells are attached, thereby binding the cells to the antibodiesand washing out unbound cells.

Further, Korean Laid-Open Patent Publication No. 2006-0068979 describesa cell separation system using an ultrasound field and traveling wavedielectrophoresis. The cell separation system includes a piezoelectrictransducer, which is connected to both ends of an upper glass substrateand may convert an electric input from the outside into a mechanicalvibration so as to be applied to the upper glass substrate; andelectrodes which are arranged on a lower substrate parallel to the upperglass substrate, the number of the electrodes being N. A fluidcontaining cells can fill the space between the upper glass substrateand the lower substrate. Each of the electrodes is disposed in avertical direction relative to the longitudinal direction of thepiezoelectric transducer and all of the N electrodes are arranged atregular intervals along the longitudinal direction of the piezoelectrictransducer.

Thus, in the above methods, specific cells are selectively concentratedor separated from a sample using specific ligands or receptorsimmobilized on a solid substrate or using an external driving force.However, a method or a device for separating cells by using theproperties of a solid support in itself and the conditions of a liquidmedium have not been reported yet.

Further, a method of removing materials preventing the cells frombinding to the solid support using ion exchange in such a method has notbeen reported yet.

SUMMARY OF THE INVENTION

The present invention provides a method of separating microorganismsusing ion exchange and a means for capturing microorganisms.

The present invention also provides a container for pretreating a samplecontaining microorganisms in the method of separating microorganisms.

The present invention also provides a device for separatingmicroorganisms using ion exchange and a means for capturingmicroorganisms.

According to an aspect of the present invention, there is provided amethod of separating microorganisms from a sample, the method including:contacting a sample containing microorganisms with an inorganic ionexchange material such that the sample reacts with the inorganic ionexchange material; and contacting the reacted sample with a means forcapturing microorganisms such that microorganisms in the sample arecaptured from the sample.

According to another aspect of the present invention, there is provideda container including an inorganic ion exchange material for pretreatinga sample containing microorganisms.

According to another aspect of the present invention, there is provideda device for separating microorganisms from a sample comprisingmicroorganisms, the device comprising: a first container comprising aninorganic ion exchange material for pretreating a sample comprisingmicroorganisms; and a second container comprising a means for capturingmicroorganisms which is in fluid communication with the first container.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and other features and advantages of the present inventionwill become more apparent by describing in detail exemplary embodimentsthereof with reference to the attached drawings in which:

FIG. 1 is a graph illustrating the effect of components of a samplecomprising E. coli cells on cell capture efficiencies using a solidsupport having an array of pillars on its surface, according to anembodiment of the present invention;

FIG. 2 is a graph illustrating the effect of various dilution ratios andflow rates on cell capture efficiencies from samples comprising E. colicells, using a solid support having an array of pillars on its surface,according to an embodiment of the present invention;

FIG. 3 is a graph illustrating the effect of zeolite treatment of urinesamples on efficiency of binding microorganisms to a solid support,according to an embodiment of the present invention;

FIG. 4 is a graph illustrating efficiency of binding microorganisms inurine samples mixed with a sodium type zeolite to a solid support,according to an embodiment of the present invention;

FIG. 5 is a graph illustrating efficiency of binding microorganisms inurine samples mixed with an ammonium type zeolite to a solid support,according to an embodiment of the present invention; and

FIG. 6 is a graph illustrating the effect of zeolite treatment ofundiluted urine samples on efficiency of binding microorganisms to asolid support, according to an embodiment of the present invention,compared to the efficiency of binding microorganisms from a urine samplediluted 1:1 with a buffer.

DETAILED DESCRIPTION OF THE INVENTION

Hereinafter, the present invention will now be described more fully withreference to the accompanying drawings, in which exemplary embodimentsof the invention are shown. The invention may, however, be embodied inmany different forms and should not be construed as being limited to theembodiments set forth herein; rather, these embodiments are provided sothat this disclosure will be thorough and complete, and will fullyconvey the concept of the invention to those skilled in the art.

According to an embodiment of the present invention, there is provided amethod of separating microorganisms from a sample, the method including:contacting a sample containing microorganisms with an inorganic ionexchange material such that the sample reacts with the inorganic ionexchange material; and contacting the reacted sample with a means forcapturing microorganisms such that microorganisms in the sample arecaptured from the sample.

The method of separating microorganisms from a sample according to thecurrent embodiment of the present invention includes contacting thesample containing microorganisms with an inorganic ion exchange materialsuch that the sample reacts with the inorganic ion exchange material.

During the contact, ion exchange and adsorption occur between the samplecontaining microorganisms and the inorganic ion exchange material.Materials which prevent microorganisms from attaching to a solid supportsuch as ionic materials and organic materials may be removed by the ionexchange and adsorption, but the method of removing the materials is notlimited thereto.

The sample containing microorganisms can be a biological sample. Theterm “biological sample” refers to a sample including or consisting ofcells or tissues, such as a biological fluid, isolated from anindividual. The individual can be an animal such as a human. Examples ofthe biological sample include saliva, sputum, blood, blood cells (suchas leukocytes and erythrocytes), amniotic fluid, serum, semen, bonemarrow, a tissue or a microneedle biopsy specimen, urine, a peritonealfluid, a pleural fluid, and cell cultures. Further, examples of thebiological sample include a tissue slice, such as a frozen tissue slicefor a histological purpose. In some embodiments, the biological sampleis blood, urine, or saliva, specifically urine.

Examples of the microorganisms in the sample can include, but are notlimited to, bacteria, fungi, and viruses.

In an embodiment of the present invention, the inorganic ion exchangematerial can be any inorganic material that has ion exchange properties.Examples of the inorganic ion exchange material can include, but are notlimited to, a zeolite, sand, and a metal oxide (e.g, SiO₂, Al₂O₃, andNa₂O). The zeolite can be an H type zeolite.

In the present embodiment, the zeolite is a crystalline aluminosilicateformed by corner-sharing tetrahedral TO₄, where T is Al or Si. Thezeolite has micropores and channels having a homogeneous molecular sizeof 1 to 20 Å, and a large surface area of about 900 m²/g. The zeolite isclassified into several types such as an H type, a NH₄ type, and a Natype zeolite, depending on the presence of a functional group capable ofbeing ionized such as H⁺, NH₄ ⁺, and Na⁺. The H type zeolite can beobtained by burning the NH₄ type zeolite at 550° C. for 2 hours, but themethod of obtaining the H type zeolite is not limited thereto. Zeolite Yis commercially available from Aldrich Chemical Co. The zeolite can be apowder or immobilized on the solid support, but the shape of zeolite isnot specifically limited.

In contacting the sample with the inorganic ion exchange materialaccording to the current embodiment of the present invention, the samplecan be contacted with the inorganic ion exchange material in a solution.The inorganic ion exchange material can be included in a container suchas a tube, a microchannel or a microchamber, or immobilized to the innerwalls of the bottom of the container. Contacting the sample with theinorganic ion exchange material can be performed at an appropriatetemperature (e.g., room temperature) for an appropriate length of time,at least 10 seconds. The experimental conditions can be modified oroptimized by those of ordinary skill in the art.

In contacting the sample with the inorganic ion exchange materialaccording to the current embodiment of the present invention, theconcentrations of cationic materials such as Na⁺ and K⁺ in the sampledecrease as a result of an ion exchange reaction between the sample andthe inorganic ion exchange material. In this way, salts which preventmicroorganisms from attaching to the solid support are removed from thesample. In addition, by contacting the sample with the inorganic ionexchange material, creatine and other materials in the sample thatprevent a polymerase chain reaction (PCR) (e.g., urea) are also removedfrom the sample by adsorption to the ion exchange material.

The method of separating microorganisms from a sample according to thecurrent embodiment of the present invention also includes contacting thereacted sample with a means for capturing microorganisms. The reactedsample indicates the sample having decreased concentration of ionicmaterials after the ion exchange reaction.

The means for capturing microorganisms can include any material thatbinds to microorganisms. Examples of the material that binds tomicroorganisms include, but are not limited to, a solid material, asemi-solid material, and a liquid material. According to an embodimentof the present invention, the means for capturing microorganisms can bea non-planar solid support.

Thus, in an embodiment, the method of separating microorganisms from asample includes: contacting a sample containing microorganisms with aninorganic ion exchange material such that the sample can react with theinorganic ion exchange material; and contacting the reacted sample witha non-planar solid support in a liquid medium having a pH of 3.0 to 6.0.

The microorganisms can attach to the non-planar solid support bycontacting the reacted sample with the non-planar solid support. It isassumed that since the surface area of the non-planar solid support islarger than that of a planar solid support and the use of the liquidmedium having a pH of 3.0 to 6.0 denatures cell membranes of themicroorganisms resulting in decreased solubility of the cell membranesin the liquid medium, the ratio of the microorganisms that attach to thesurface of the non-planar solid support increases under such conditions.However, the scope of the present invention is not limited to thisspecific mechanism.

In contacting the reacted sample with the non-planar solid supportaccording to the current embodiment of the present invention, thereacted sample may be diluted with a buffer solution capable ofbuffering the microorganisms at a low pH. The buffer may be a phosphatebuffer (such as, sodium phosphate, pH 3.0 to 6.0) or an acetate buffer(such as, sodium acetate, pH 3.0 to 6.0). The sodium phosphate buffermay be 10 mM to 500 mM sodium phosphate buffer, preferably, 50 mM to 300mM sodium phosphate buffer. The sodium acetate buffer may be 10 mM to500 mM sodium acetate buffer, preferably, 50 mM to 300 mM sodium acetatebuffer. The dilution ratio of the sample with the buffer may be 99:1 to1:1,000, preferably 99:1 to 1:10, more preferably 99:1 to 1:4, but isnot limited thereto.

In contacting the reacted sample with the non-planar solid supportaccording to the current embodiment of the present invention, thereacted sample may have a salt at a concentration of 10 to 500 mM, andpreferably 50 to 300 mM. The salts include the salts contained in thebuffer solution, such as acetate salts or phosphate salts. The reactedsample may have an ion selected from the group consisting of acetate andphosphate at a concentration of 10 to 500 mM, and preferably 50 to 300mM.

In contacting the reacted sample with the non-planar solid supportaccording to the current embodiment of the present invention, thenon-planar solid support has a larger surface area than a planar solidsupport. The non-planar solid support can have an uneven structure onits surface. The term “uneven structure” used herein indicates that thesurface of the structure is not smooth and has areas that can be concaveor convex. The uneven structure can have a surface having a plurality ofpillars or a surface having a sieve-like structure with a plurality ofpores, but the present invention is not limited thereto.

The non-planar solid support can have any shape and can be a solidsupport having a plurality of pillars on its surface, a solid support inthe form of a bead, or a solid support having a sieve structure with aplurality of pores on its surface. The non-planar solid support can beused alone or in an assembly of a plurality of solid supports (forexample, an assembly in a tube or a container).

The non-planar solid support can be a tube, a microchannel of amicrofluidic device, or an inner wall of a microchamber. Thus, themethod of separating microorganisms from a sample according to thecurrent embodiment of the present invention can be performed in afluidic device or a microfluidic device having at least one inlet andoutlet, wherein the inlet and outlet are in fluid communication witheach other through a channel or a microchannel.

As used herein, the term “microfluidic device” incorporates the conceptof a microfluidic device that comprises microfluidic elements such as,e.g., microfluidic channels (also called microchannels or microscalechannels). As used herein, the term “microfluidic” refers to a devicecomponent, e.g., chamber, channel, reservoir, or the like, that includesat least one cross-sectional dimension, such as depth, width, length,diameter, etc. of from about 0.1 micrometer to about 1000 micrometer.Thus, the term “microchamber” and “microchannel” refer to a channel anda chamber that includes at lest one cross-sectional dimension, such asdepth, width, and diameter of from about 0.1 micrometer to about 1000micrometer, respectively.

In an embodiment, the non-planar solid support can be a solid supporthaving a plurality of pillars on its surface. A method of formingpillars on a solid support is well known in the art. For example, aplurality of fine pillars in a high-density structure can be formed on asolid support using photolithography, etc. used in manufacturingsemiconductors. The pillars can have an aspect ratio (the height of thepillar:the length of a cross section of the pillar) of 1:1 to 20:1, butthe aspect ratio is not limited thereto. The term “aspect ratio” usedherein refers to the ratio of the height of the pillar to the length ofa cross section of a pillar. When the cross section is a circle, thelength of the cross section refers to the diameter of the circle, andwhen the cross section is a rectangle, the length of the cross sectionrefers to the average length of each side of the rectangle. The ratio ofthe height of the pillars to the distance between the pillars (height:distance) can be 1:1 to 25:1. The distance between the pillars can be 5to 100 μm, preferably 5 to 50 μm.

The non-planar solid support can be hydrophobic with a water contactangle of 70 to 95°. The hydrophobicity can be provided by coating asurface of the non-planar solid support with a compound selected fromthe group consisting of octadecyldimethyl (3-trimethoxysilylpropyl)ammonium (OTC) and tridecafluorotetrahydrooctyltrimethoxysilane(DFS). For example, a SiO₂ layer of a non-planar solid support can becoated with a self-assembled monolayer (SAM) of a compound selected fromthe group consisting of OTC and DFS to provide a water contact angle of70 to 95°. In this application, the term “water contact angle” refers towater contact angle measured by a Kruss Drop Shape Analysis System typeDSA 10 Mk2. A droplet of 1.5 μl deionized water is automatically placedon the sample. The droplet was monitored every 0.2 seconds for a periodof 10 seconds by a CCD-camera and analyzed by Drop Shape Analysissoftware (DSA version 1.7, Kruss). The complete profile of the dropletwas fitted by the tangent method to a general conic section equation.The angles were determined both at the right and left side. An averagevalue is calculated for each drop and a total of five drops per sampleare measured. The average of the five drops is taken the contact angle.

The non-planar solid support can have at least one amine-basedfunctional group on its surface. The surface of the non-planar solidsupport having the at least one amine-based functional group can beprepared by coating the surface of the non-planar solid support withpolyethyleneiminetrimethoxysilane (PEIM). For example, a SiO₂ layer of anon-planar solid support may be coated with a SAM of PEIM. Theamine-based functional group is positively charged at a pH of 3.0 to6.0.

The solid substrate can be a substrate formed of any kind of materialthat has a water contact angle of 70 to 95° or has at least oneamine-based functional group at its surface, or of any kind of materialwhich has a surface which may be coated as described above to obtain awater contact angle of 70 to 95° or to have at least one amine-basedfunctional group at its surface. Examples of the material used to formthe non-planar solid support include, but are not limited to, glass,silicon wafer, and plastics, etc.

It is assumed that when the sample containing microorganisms contactsthe non-planar solid support having a surface having a water contactangle of 70 to 95° or a surface having at least one amine-basedfunctional group on its surface, the microorganisms attach to thesurface of the non-planar solid support. However, the range of thepresent invention is not limited to this specific mechanism.

The method of separating microorganisms from a sample according to thecurrent embodiment of the present invention may further include washingout substances, other than the target microorganisms, that are notattached to the non-planar solid support after contacting the reactedsample with the non-planar solid support. In the washing, any washingsolution that does not separate the attached target microorganisms fromthe surface of the non-planar solid support but is capable of removingimpurities from the sample that can adversely affect subsequentprocesses may be used. For example, the washing solution can be anacetate buffer or a phosphate buffer used as a binding buffer, etc. Thatis, the sodium phosphate buffer may be 10 mM to 500 mM sodium phosphatebuffer, preferably, 50 mM to 300 mM sodium phosphate buffer. The sodiumphosphate buffer may be 10 mM to 500 mM sodium phosphate buffer,preferably, 50 mM to 300 mM sodium phosphate buffer. The washingsolution can be a buffer having a pH of 3.0 to 6.0.

The term “separating microorganisms” used herein refers to concentrationof the microorganisms or isolation of pure microorganisms.

In the method of separating microorganisms from a sample according tothe current embodiment of the present invention, the microorganismsconcentrated by attachment to the non-planar solid support can besubjected to a subsequent process, such as isolation of DNA.Alternatively, the microorganisms concentrated by attachment to thenon-planar solid support can be eluted from the non-planar solid supportand then subjected to a subsequent process, such as isolation of DNA.

Thus, the method of separating microorganisms from a sample according tothe current embodiment of the present invention may further includeeluting the attached microorganisms from the non-planar solid supportafter contacting the reacted sample with the non-planar solid supportand/or washing. In eluting the microorganisms from the solid supportaccording to the current embodiment of the present invention, theeluting solution may be any known solution that can detach themicroorganisms from the non-planar solid support. Examples of theeluting solution include water and Tris buffer, preferably 10 mM to 1000mM Tris buffer. The eluting solution may have a pH of 6.0 or greater.

According to another embodiment of the present invention, there isprovided a method of treating microorganisms. The method of treatingmicroorganisms includes subjecting the microorganisms separated usingthe method of separating microorganisms from a sample disclosed hereinto at least one process selected from: isolation of a nucleic acid, anamplification reaction of a nucleic acid, and a hybridization reactionof a nucleic acid. The isolation of a nucleic acid, the amplificationreaction of a nucleic acid, and the hybridization reaction of a nucleicacid can be performed using any methods known in the art.

According to another embodiment of the present invention, there isprovided a container including an inorganic ion exchange material forpretreating a sample containing microorganisms.

In the container, the inorganic ion exchange material may be anyinorganic material that has ion exchange properties. Examples of theinorganic ion exchange material can include, but are not limited to, azeolite, sand, and a metal oxide (e.g, SiO₂, Al₂O₃, and Na₂O). Thezeolite can be an H type zeolite. Zeolites were described above.

The container can be a tube, a microchannel, or a microchamber. Theinorganic ion exchange material can be included in the container orimmobilized on the inner walls of the bottom of the container. Thecontainer can include an inlet and an outlet through which a sample isinjected and discharged. In addition, the container may be amicrofluidic device or a lab-on-a-chip including a microchannel and amicrochamber.

The container is used for a sample pretreatment process to removematerials from the sample that prevent cells in the sample fromattaching to a solid support. The sample pretreatment process comprisescontacting a sample containing microorganisms with the inorganic ionexchange material in the container.

According to another embodiment of the present invention, there isprovided a device for separating microorganisms from a sample havingmicroorganisms, the device including: a first container including aninorganic ion exchange material for pretreating the sample containingmicroorganisms; and a second container including a means for capturingmicroorganisms, which is in fluid communication with the firstcontainer.

In the device for separating microorganisms from a sample, the firstcontainer including an organic ion exchange material for thepretreatment of the sample containing microorganisms is in fluidcommunication with the second container including the means forcapturing microorganisms.

In the first container, the inorganic ion exchange material may be anyinorganic material that has ion exchange properties. Examples of theinorganic ion exchange material were described above.

The inorganic ion exchange material may be included in the firstcontainer or immobilized on the inner walls of the bottom of the firstcontainer. The first container can be a tube, a microchannel, or amicrochamber including the inorganic ion exchange material or to whichthe inorganic ion exchange material is immobilized. The first containercan include an inlet and an outlet through which a sample is injectedand discharged. The first container can also be a microfluidic device ora lab-on-a-chip including a microchannel and a microchamber.

The first container is used for a sample pretreatment process to removematerials from a sample that prevent cells in the sample from attachingto the solid support by contacting the sample containing microorganismswith the inorganic ion exchange material in the first container.

In the device for separating microorganisms from a sample according tothe current embodiment of the present invention, the second container isin fluid communication with the first container. In addition, the devicemay further include a valve and a pump in a portion for connecting thefirst container and the second container, and thus for controlling theamount of the sample moving from the first container to the secondcontainer.

The means for capturing microorganisms included in the second containermay attach microorganisms to its surface based on properties of thesample containing microorganisms, such as the concentration and pH.

The means for capturing microorganisms may include any material thatbinds to microorganisms as described above. The means for capturingmicroorganisms can be a non-planar solid support.

In an embodiment, the device for separating microorganisms from a sampleincludes: a first container including an inorganic ion exchange materialfor pretreating a sample containing microorganisms; and a secondcontainer including a non-planar solid support, wherein the secondcontainer is in fluid communication with the first container.

The non-planar solid support suitable for the second container is asdescribed above. The non-planar solid support has a larger surface areathan a planar solid support. The non-planar solid support can have anuneven structure on its surface. The uneven structure may have a surfacehaving a plurality of pillars or a surface having a sieve-like structurewith a plurality of pores, but the present invention is not limitedthereto.

The non-planar solid support included in the second container can haveany shape and can be a solid support having a plurality of pillars onits surface, a solid support in the form of a bead, or a solid supporthaving a sieve structure with a plurality of pores on its surface. Thenon-planar solid support may be used alone or in an assembly of aplurality of the solid supports (for example, an assembly in a tube or acontainer).

The non-planar solid support included in the second container may be atube, a microchannel of a microfluidic device or an inner wall of amicrochamber. Thus, the second container can include at least one inletand outlet and can be a fluidic device or a microfluidic device havingat least one inlet and outlet, wherein the inlet and outlet are in fluidcommunication with each other through a channel or a microchannel. Thesecond container may also be a lab-on-a-chip including the non-planarsolid support or to which the non-planar solid support is immobilized.In an embodiment of the present invention, the second container isfilled with a non-planar solid support in the form of beads.

The non-planar solid support included in the second container can be asolid support having a plurality of pillars on its surface. The pillarscan have an aspect ratio (the height of the pillar:the length of thecross-section of the pillar) of 1:1 to 20:1, but the aspect ratio is notlimited thereto. The ratio of the height of the pillars to a distancebetween the pillars (height:distance) can be 1:1 to 25:1. The distancebetween the pillars can be 5 to 100 μm, preferably 5 to 50 μm.

The non-planar solid support included in the second container may havehydrophobicity with a water contact angle of 70 to 95°. Thehydrophobicity may be provided as described above.

The non-planar solid support included in the second container can haveat least one amine-based functional group on its surface. The supportmay be coated with PEIM to provide a surface having the at least oneamine-based functional group as described above.

The non-planar solid support included in the second container can beformed of any material having a water contact angle of 70 to 95°, anymaterial having at least one amine-based functional group on itssurface, or any material which has a surface which may be coated, asdescribed above, to obtain a water contact angle of 70 to 95° or to haveat least one amine-based functional group at its surface. Examples ofthe material used to form the non-planar solid support include, but arenot limited to, glass, silicon wafer, and plastics, etc.

Hereinafter, the present invention will be described in more detail withreference to the following examples. However, these examples are forillustrative purposes only and are not intended to limit the scope ofthe invention.

EXAMPLES Example 1 Concentrating E. coli Cells in a Urine MimeticSolution Using a Solid Support Having an Array of Pillars on itsSurface—Screening Factors Preventing Capture of Cells

A sample containing E. coli cells was allowed to flow through a fluidicdevice including a chamber having an inlet and an outlet and having asurface of a silicon chip having an area of 10 mm×23 mm on which anarray of pillars was formed, thereby attaching the cells to the surfaceof the solid support. The number of the bacteria cells in the sampledischarged from the fluidic device was determined using colony counting,and then an efficiency of capturing the bacteria cells by the solidsupport was calculated using the counted number of colonies. In thearray of pillars, the distance between the pillars was 12 μm, the heightof the pillars was 100 μm, and a cross section of each of the pillarswas in the form of a square having sides of 25 μm.

The array of pillars was formed on a SiO₂ layer coated with aself-assembled monolayer (SAM) of octadecyldimethyl (3-trimethoxysilylpropyl)ammonium (OTC).

Solutions based on a sodium acetate buffer and solutions based ondialyzed urine, both containing 0.01 OD₆₀₀ of E. coli cells, were usedas the cell sample.

The solutions based on a sodium acetate buffer (pH 4.0) are as follows:

Buffer: a 100 mM sodium acetate buffer (pH 4.0),

Buffer+salt: a solution having the concentrations of the salts of 88 mMNaCl, 67 mM KCl, 38 mM NH₄Cl, and 18 mM Na₂SO₄, which was obtained byadding 0.514 g NaCl, 0.5 g KCl, 0.203 g NH₄Cl, and 0.259 g Na₂SO₄ to a100 mM sodium acetate buffer (pH 4.0),

Buffer+salt+urea: a solution obtained by adding 333 mM urea to the“Buffer+salt” solution,

Buffer+salt+urea+creatine: a solution obtained by adding 333 mM urea and9.8 mM creatine to the “Buffer+salt” solution,

Buffer+salt+urea+creatine+uric acid: a solution obtained by adding 333mM urea, 9.8 mM creatine, and 2.5 mM uric acid to the “Buffer+salt”solution, and

Buffer+salt+urea+creatine+uric acid+glucose: a solution obtained byadding 333 mM urea, 9.8 mM creatine, 2.5 mM uric acid, and 0.6 mMglucose to the “Buffer+salt” solution.

The solutions based on dialyzed urine were obtained by mixing dialyzedurine and a 2×-concentrated solution of—each of the solutions abovebased on the sodium acetate buffer in a ratio of 1:1. The final pH ofthese solutions was 3.97.

200 μl of each of the samples was allowed to flow from the inlet to theoutlet through the chamber at a flow rate of 200 μl/min. The experimentswere repeated three times. The number of cells in each of the sampleswas counted before and after the samples flowed through the chamberhaving the solid support.

FIG. 1 is a graph illustrating cell capture efficiencies as a functionof solution conditions for separating E. coli cells from the varioustested samples using a solid support having an array of pillars on itssurface according to an embodiment of the present invention. Referringto FIG. 1, when salts or other substances were added to the buffer orthe buffer:dialyzed urine (1:1) sample, the cell capture efficienciesdecreased relative to the cell capture efficiency determined for thebuffer or the buffer:dialyzed urine (1:1) sample. Note also that thecell capture efficiency of the buffer:dialyzed urine (1:1) sample wassmaller than that for the buffer sample, suggesting that dialyzed urinecontains materials that interfere with cell attachment to the solidsupport.

Example 2 Concentrating E. coli Cells in a Urine Solution Using a SolidSupport Having an Array of Pillars on its Surface—Determination ofEffects of Dilution Ratio of Urine and Flow Rate on Concentrating theCells

A sample containing E. coli cells was allowed to flow through a fluidicdevice including a chamber having an inlet and an outlet and having asurface of a silicon chip having an area of 10 mm×23 mm on which anarray of pillars was formed, thereby attaching the cells to the surfaceof the solid support. The number of the bacteria cells in the sampledischarged from the fluidic device was determined using colony counting,and then an efficiency of capturing the bacteria cells by the solidsupport was calculated using the counted number of colonies. Thedimensions of the array of pillars were identical to the array describedin Example 1. However, in the current example, the surface of the arrayof pillars had a SAM coating of PEIM coated on a SiO₂ layer.

Samples were prepared as follows. A buffer and urine were mixed invarious dilution ratios to obtain a final volume of 1 ml. Then, 10 μl of1.0 OD E. coli cells was added to each of the resulting mixtures.

200 μl of each of the diluted urine samples was allowed to flow from theinlet to the outlet through the chamber at a fixed flow rate (100, 300,or 500 μl/min). The experiments were repeated three times. The number ofcells in each of the samples was counted before and after the samplesflowed through the chamber having the solid support.

FIG. 2 is a graph illustrating cell capture efficiencies at variousdilution ratios and flow rates for concentrating E. coli cells using asolid support having an array of pillars on its surface, according to anembodiment of the present invention. Referring to FIG. 2, at a fixedflow rate, as the dilution ratio of the urine samples increased, thecell capture efficiency increased, and at a fixed dilution ratio, as theflow rate increased, the cell capture efficiency decreased.

As described in Examples 1 and 2, materials preventing microorganismsfrom attaching to the solid support, such as ionic substances andcreatine, are present in the urine samples. Further, when the urine wasdiluted with a high dilution ratio of generally 5 or greater, theefficiency of capturing the microorganisms by the solid support washigh. Therefore, when it is intended to separate the microorganisms fromurine using a solid support, these materials should be removed from theurine samples to optimize capture efficiency in the separation process.

Example 3 Effects of Zeolite Treatment on Binding Microorganisms to aSolid Support

Zeolite Y (Aldrich Chemical Co.) (NH₄—Y type) was burned at 550° C. for2 hours to prepare HY (H type zeolite).

30 μl of urine was mixed with 0.3 g of the obtained H type zeolite, andthe mixture was mixed with 200 mM of acetate buffer (pH 3.0) (1:1 v/v).Then, E. coli cells were added to the mixture to obtain an OD value of0.01. The control group was prepared in the same manner as above, exceptthat zeolite was not added. Two types of urine were used. The pH of theurine sample (initially having a typical pH ranging from about 5 toabout 8) decreased after being mixed with zeolite. For the specificurine samples used in this example, the initial pH values of urine 1: pH6.2 and urine 2: pH 6.8 were reduced to a pH of 4. The pH of the controlgroup remained unchanged (urine 1: pH 6.2 and urine 2: pH 6.8). Thus, itwas assumed that ion exchange occurred in the samples containing theH-type zeolite.

The ion exchanged urine sample was diluted, and contacted with anon-planar solid support to attach microorganisms in the sample to thenon-planar solid support. Then, a cell binding efficiency from each ofthe urine samples was measured.

Ion exchanged urine samples containing E. coli cells were allowed toflow through a fluidic device including a chamber having an inlet and anoutlet and having a surface of a silicon chip having an area of 10 mm×23mm on which an array of pillars was formed, thereby attaching the cellsto the surface of the solid support. The number of the E. coli cells inthe sample discharged from the fluidic device was determined by opticaldensity determination, and then an efficiency of capturing the E. colicells by the solid support was calculated using the determined number ofthe cells. The dimensions of the array of pillars were as described inExample 1. The surface of the array of pillars had a SAM coating of PEIMcoated on a SiO₂ layer.

200 μl of each of the samples was allowed to flow from the inlet to theoutlet through the chamber at a flow rate of 200 μl/min. The experimentswere repeated two times for each sample. In FIGS. 3-6, C1 and C2respectively stand for chip 1 and chip 2, for repetition experiments;the black or white bars represent repetition experiments for cellbinding efficiency for the same sample type. The cell binding efficiencyrepresents initial cell numbers/unit area—recovered cell numbers/unitarea, wherein the initial cell numbers/unit area and recovered cellnumbers/unit area represent cell numbers before flowing through the chipand cell numbers after flowing through the chip, respectively. Thenumber of cells were counted by a colony counting method and the blackor white bar data were obtained by colony counting after diluting1/40,000 and 1/80,000 the sample, respectively. FIG. 3 is a graphillustrating the effect of zeolite treatment of urine samples onefficiency of binding microorganisms to the solid support, according toan embodiment of the present invention. Referring to FIG. 3, the samplestreated with zeolite had remarkably greater cell binding efficienciesthan the samples not treated with zeolite. In particular, for the set ofsamples labeled “urine 1”, the urine samples had low cell bindingefficiencies, and the zeolite treatment resulted in a significantincrease in the cell binding efficiency observed for each sample. Thus,it is considered that a specific level of cell binding efficiency can beobtained after zeolite treatment, independent of urine.

Example 4 Effects of Zeolite Treatment on Binding Microorganisms to aSolid Support: Effects of NaY Type and NH₄Y Type Zeolite

A sodium type zeolite Na—Y and an ammonium type zeolite NH₄—Y wereobtained from Aldrich Chemical Co.

30 μl of urine was mixed with 0.3 g of either the sodium type zeolite orthe ammonium type zeolite. Each zeolite-treated urine was then mixedwith 200 mM of acetate buffer (pH 3.0) (1:1 v/v). Then, E. coli cellswere added to the mixture to obtain an OD value of 0.01. The controlgroup was prepared in the same manner as above except that zeolite wasnot added. Two types of urine were used. The pH of the urine samplesremained unchanged, with the samples based on the two urine types havinga pH of 6.2 or 7.0, respectively, after treatment with the NaY typezeolite, and a pH or 5.9 or 6.5, respectively, after treatment with theNH₄Y type zeolite.

The mixture of the urine sample and zeolite was contacted with anon-planar solid support to attach microorganisms in the mixture to thenon-planar solid support. Then, a cell binding efficiency from each ofthe urine samples was measured.

Urine samples containing ion exchanged E. coli cells were allowed toflow through a fluidic device including a chamber having an inlet and anoutlet and having a surface of a silicon chip having an area of 10 mm×23mm on which an array of pillars was formed, thereby attaching the cellsto the surface of the solid support. The number of the E. coli cells inthe sample discharged from the fluidic device was determined by opticaldensity determination, and then an efficiency of capturing the E. colicells by the solid support was calculated using the determined number ofthe cells. The dimensions of the array of pillars were as described inExample 1. The surface of the array of pillars had a SAM coating of PEIMcoated on a SiO₂ layer.

200 μl of each of the urine samples was allowed to flow from the inletto the outlet through the chamber at a flow rate of 200 μl/min. Theexperiments were repeated two times with each type of urine sample.

The efficiency of binding microorganisms in the urine samples mixed withthe sodium type zeolite or the ammonium type zeolite to a solid supportis shown in FIG. 4 or FIG. 5, respectively. Referring to FIGS. 4 and 5,the samples treated with the sodium type zeolite and the ammonium typezeolite had similar or smaller cell binding efficiencies compared to thesamples not treated with zeolite. Thus, it is inferred that the pHdecrease due to H+ ions obtained from the ion exchange between the Htype zeolite and urine sample has an advantageous effect on the cellbinding efficiency.

Example 5 Effects of Zeolite Treatment on Binding Microorganisms to aSolid Support: Comparison Between a Diluted Sample and an UndilutedSample Treated with Zeolite

Zeolite Y (Aldrich Chemical Co.) (NH4-Y type) was burned at 550° C. for2 hours to prepare HY (H type zeolite).

30 μl of urine was mixed with 0.3 g of the obtained H type zeolite(undiluted urine sample). 30 μl of urine was mixed with 200 mM ofacetate buffer (pH 3.0) (1:1 v/v) to prepare a control group (two timesdiluted urine sample). Then, E. coli cells were added to each mixture toobtain an OD value of 0.01. One type of urine sample was used. The pH ofthe urine sample mixed with the zeolite decreased after mixing with thezeolite from an initial pH of 7.4 to a pH of 3.8. It is assumed that ionexchange occurred. The pH of the control group decreased to pH 4.2 dueto the dilution with the buffer.

The ion exchanged urine sample and the control were each contacted witha non-planar solid support to attach microorganisms in the samples tothe non-planar solid support. Then, a cell binding efficiency of each ofthe samples was measured.

Ion exchanged urine samples or the control samples containing E. colicells were allowed to flow through a fluidic device including a chamberhaving an inlet and an outlet and having a surface of a silicon chiphaving an area of 10 mm×23 mm on which an array of pillars was formed,thereby attaching the cells to the surface of the solid support. Thenumber of E. coli cells in the sample discharged from the fluidic devicewas also determined by optical density determination, and then anefficiency of capturing the E. coli cells by the solid support wascalculated using the determined number of the cells. The dimensions ofthe array of pillars were as described in Example 1. The surface of thearray of pillars had a SAM coating of PEIM coated on a SiO₂ layer.

200 μl of each of the urine samples was allowed to flow from the inletto the outlet through the chamber at a flow rate of 200 μl/min. Theexperiments were repeated two times.

FIG. 6 is a graph illustrating the effect of zeolite treatment of urinesamples without dilution on efficiency of binding microorganisms to thesolid support, according to an embodiment of the present invention.Referring to FIG. 6, the ion exchanged samples without dilution hadremarkably greater cell binding efficiencies than the diluted samples.That is, a cell binding efficiency of about 25% of could be obtainedafter ion exchange without requiring a volume increase in the sampleresulting from dilution.

By using the method of separating microorganisms such as bacteria,fungi, or viruses from a biological sample according to the presentinvention, the microorganisms may be efficiently separated from thebiological sample.

By using the container for pretreating a sample containingmicroorganisms according to the present invention, the efficiency ofbinding microorganisms to the solid support may increase.

Further, by using the device for separating microorganisms such asbacteria, fungi, or viruses from a biological sample according to thepresent invention, the microorganisms may be efficiently separated fromthe biological sample.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention.The terms “a” and “an” do not denote a limitation of quantity, butrather denote the presence of at least one of the referenced item. Theterm “or” means “and/or”. The terms “comprising”, “having”, “including”,and “containing” are to be construed as open-ended terms (i.e., meaning“including, but not limited to”).

Recitation of ranges of values are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein. The endpoints of all ranges are includedwithin the range and independently combinable.

All methods described herein can be performed in a suitable order unlessotherwise indicated herein or otherwise clearly contradicted by context.The use of any and all examples, or exemplary language (e.g., “suchas”), is intended merely to better illustrate the invention and does notpose a limitation on the scope of the invention unless otherwiseclaimed. No language in the specification should be construed asindicating any non-claimed element as essential to the practice of theinvention as used herein. Unless defined otherwise, technical andscientific terms used herein have the same meaning as is commonlyunderstood by one of skill in the art to which this invention belongs.

Preferred embodiments of this invention are described herein, includingthe best mode known to the inventors for carrying out the invention.Variations of those preferred embodiments may become apparent to thoseof ordinary skill in the art upon reading the foregoing description. Theinventors expect skilled artisans to employ such variations asappropriate, and the inventors intend for the invention to be practicedotherwise than as specifically described herein. Accordingly, thisinvention includes all modifications and equivalents of the subjectmatter recited in the claims appended hereto as permitted by applicablelaw. Moreover, any combination of the above-described elements in allpossible variations thereof is encompassed by the invention unlessotherwise indicated herein or otherwise clearly contradicted by context.

While the present invention has been particularly shown and describedwith reference to exemplary embodiments thereof, it will be understoodby those of ordinary skill in the art that various changes in form anddetails may be made therein without departing from the spirit and scopeof the present invention as defined by the following claims.

1. A device for separating microorganisms from a urine sample containingmicroorganisms, the device comprising: a first container comprising anH-type zeolite for pretreating a urine sample comprising microorganisms,wherein the H-type zeolite is immobilized on the first container; and asecond container comprising a non-planar solid support to whichmicroorganisms can bind, which is in fluid communication with the firstcontainer, wherein the non-planar solid support is a solid supporthaving hydrophobicity with a water contact angle of 70 to 95° or havingat least one amine-based functional group on its surface.
 2. The deviceof claim 1, wherein the first and second containers are selected fromthe group consisting of a tube, a microchannel, and a microchamber. 3.The device of claim 1, wherein the second container further comprises abuffer solution storage unit.
 4. The device of claim 1, wherein thenon-planar solid support is a solid support having a plurality ofpillars on its surface, the non-planar solid support is held within thesecond container and is in the form of a bead, or the non-planar-solidsupport has a sieve structure with a plurality of pores on its surface.5. The device of claim 4, wherein the pillars have an aspect ratio of1:1 to 20:1, wherein the aspect ratio is a height of the pillar to alength of a cross section of the pillar.
 6. The device of claim 4,wherein the ratio of the height of the pillars to the distance betweenthe pillars is 1:1 to 25:1.
 7. The device of claim 4, wherein thedistance between the pillars is 5 to 100 μm.
 8. The device of claim 1,wherein the hydrophobicity is provided by a surface of the non-planarsolid support coated with octadecyldimethyl (3-trimethoxysilylpropyl)ammonium (OTC) or tridecafluorotetrahydrooctyltrimethoxysilane(DFS).
 9. The device of claim 1, wherein the surface having the at leastone amine-based functional group is prepared by coating the surface withpolyethyleneiminetrimethoxysilane (PEIM).